Merge branch 'master' into toil-prov

Author: mr-c

cwltool/main.py

@@ -850,6 +850,8 @@ def remove_at_id(doc):  # type: (MutableMapping[Text, Any]) -> None
                                         if isinstance(entry, MutableMapping):
                                             remove_at_id(entry)
                     remove_at_id(out)
+                    visit_class(out, ("File",), functools.partial(
+                        add_sizes, runtimeContext.make_fs_access('')))
 
                 def loc_to_path(obj):  # type: (Dict[Text, Any]) -> None
                     for field in ("path", "nameext", "nameroot", "dirname"):

cwltool/provenance.py

@@ -804,10 +804,13 @@ def used_artefacts(self,
                 base += "/" + name
             for key, value in job_order.items():
                 prov_role = self.wf_ns["%s/%s" % (base, key)]
-                entity = self.declare_artefact(value)
-                self.document.used(
-                    process_run_id, entity, datetime.datetime.now(), None,
-                    {"prov:role": prov_role})
+                try:
+                    entity = self.declare_artefact(value)
+                    self.document.used(
+                        process_run_id, entity, datetime.datetime.now(), None,
+                        {"prov:role": prov_role})
+                except OSError:
+                    pass
 
     def generate_output_prov(self,
                              final_output,    # type: Union[Dict[Text, Any], List[Dict[Text, Any]]]
@@ -1580,7 +1583,10 @@ def _relativise_files(self, structure):
                 del structure["location"]
 
             for val in structure.values():
-                self._relativise_files(val)
+                try:
+                    self._relativise_files(val)
+                except OSError:
+                    pass
             return
 
         if isinstance(structure, (str, Text)):